Update deprecated and rename

util/README.md

@@ -1,5 +1,13 @@
 # Utility scripts
 
+## Check tool directory names
+
+Verify that the path of all tools contains the name of the corresponding tool shed repository:
+
+```bash
+./util/check_directory_names.py
+```
+
 ## Use case: An input TIFF file is too large
 
 Assuming that the TIFF file is an RGB file:

util/check_directory_names.py

@@ -0,0 +1,26 @@
+#!/bin/env python
+
+import glob
+import pathlib
+import yaml
+
+
+gia_root_path = pathlib.Path(__file__).resolve().parent.parent
+gia_root_dir_names = [gia_root_path.name] + [p.name for p in gia_root_path.parents if p.name != '']
+
+
+for path_str in glob.glob('./**/.shed.yml', recursive=True):
+
+    # Read the .shed.yml file:
+    shed_file_path = pathlib.Path(path_str).resolve()
+    with shed_file_path.open('r') as shed_file:
+        shed = yaml.safe_load(shed_file)
+        ts_repo_name = shed['name']
+
+    # Check that the toolshed repo name corresponds to one of the parent directory names:
+    parent_dir_names = frozenset(p.name for p in shed_file_path.parents if p.name != '') - frozenset(gia_root_dir_names)
+    if ts_repo_name not in parent_dir_names:
+        print(
+            f'{shed_file_path.relative_to(gia_root_path)}: '
+            f'{ts_repo_name} not in {", ".join(str(dir_name) for dir_name in parent_dir_names)}'
+        )